A talented crew of researchers led by Dr. Yuval Ebenstein (Tel-Aviv University, Israel) recently pioneered a technique that gives anyone the ability to assay 5hmc “nanodrop” style. In their paper, they presented proof-of-principle experimentation. They labeled DNA and then sandwiched it between two glass slides to stretch it.. The DNA was then imaged on a fluorescent microscope and 5hmC sites were counted as red spots along the DNA. This gave the exact 5hmC to nucleotide ratio in the sample.
Here’s what they showed (along with explanations from Dr. Ebenstein):
- This first direct visualization of individual epigenetic modifications in the genome. (“This is a technical and conceptual breakthrough as it allows not only to quantify the amount of modified bases but also to pin point and map their position in the genome.”)
- Single molecule detection offers the most sensitive detection of genomic hydroxymethylcytosine ever reported. (“Opening research into numerous human cell types (including human blood cells) not accessible due to low levels of epigenetic modification.”)
- A simple and quick UV-vis measurement can replace tedious radioactive, mass-spec and affinity based methods existing today. (“Basically enabling any lab equipped with a UV-vis spectrophotometer to quantify hydroxymethylation levels.”)
“It will be great to simultaneously get genetic information on the single molecule level and the overlaying epigenetic patterns of the same molecule”, says Dr. Ebenstein. “This is where I think things should go, full genetic and epigenetic profiling of individual genomes. It seems that the technology is finally ripe to tackle such challenges.”
“It has amazing sensitivity and it isn’t rocket science”, says Dr. Ebenstein. “The uv-vis absorption method for global quantification is very easy to apply and anyone with a nanodrop or the like can perform the measurements with small amounts of sample. All the reagents are commercially available but I hope someone turns it into a kit which will make it more accessible.”
Read all about it in Chemical Communications.